National Aeronautics and Space Administration currently works on building the interplanetary network which expands the terrestrial internet functionality into outer space. Delay Tolerant Networking (DTN) is an advanced technology that can overcome the problems in space communication including long propagation, frequent link disruption, high error rate, and others. Interplanetary overlay network (ION) software is an implementation of DTN architecture specially designed for communication between astronomical bodies. ION software was tested with DINET (Deep Impact Network) to validate its protocols (November 2008). However, there is not much work done to evaluate the performance of ION protocols in space operation. In this thesis, we present an experimental evaluation of ION protocols including BP/TCPCL/UDP, BP/LTPCL/UDP, and BP/UDPCL/LDP running on top of TCP/IP over a long delay interplanetary communication link with a focus on a performance comparison of primary and secondary relay paths. Different convergence layer protocols are used for links between the moon, Earth, and a relaying orbiter. We hope the results of this experiment will help us choose better combination of protocols used for a secondary path.